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Identifying Evolutionary Diversity of Indian wolf through Next Generation Sequencing

GENOME July 31, 2018LRB

Indian wolf (Canis lupus pallipes, synonym Canis indica), a subspecies of grey wolf (Canis lupus) is known to inhabit areas ranging from Southwest Asia to the Indian Subcontinent. These animals are intermediate in size between Arabian and Himalayan (Tibetan) wolf and possess no luxuriant winter coat found in other wolves residing in cold climate (1). However, they have short but less dense coat than other species of wolves, which is very fitting to their needs for survival under warm locations. In India, they dwell in habitats such as scrub-lands, thorn forests, arid and semi-arid grassland of Uttar Pradesh, Gujarat, Maharashtra and Karnataka (2). They survive by feeding on small animals, including rodents, raccoons and rabbits. Usually, they hunt during evening or night time. Indian wolf is also known to kill livestock and attack humans, hence, has become an enemy of the people in those regions. This behavior is mainly due to their lack of food in their natural environment as explained by experts.

In recent years, their population has significantly reduced and now they are considered as endangered. At present, only about 3,000 Indian wolves are believed to be present in the wild. Thus, they are protected by keeping in captivity at few locations such as the Jai Samand Sanctuary in Rajasthan. Because of their bad reputation and deprived monetary area where they live, conserving these animals is a major challenge. As most Indian wolves exist outside of protected Areas, and due to reduced natural prey species, they are forced to feed on livestock. This has resulted in conflict with local population leading to their reciprocal killings (3). Although they are protected due to being endangered, hunting still continues even today. With only a limited population left, it is obligatory to conserve Indian wolf species and to facilitate their breeding to increase their numbers.

Indian wolf (Canis lupus pallipes, synonym Canis indica)

They are suspected to have originated from the main ancestors of domestic dogs (4). Also, it is guessed that their challenging behavior with society would have led to their domestication as present day dogs and possibly towards their extinction. Due to the reddish to light brown color of the body, Indian wolf is sometimes confused as a fox when observed in the wild. However, some people erroneously speculate that Indian wolves to be grouped into a separate species. These wolves are not morphologically distinct from other Indian pallipes, and they don’t behave differently from them either. Thus, a lot of confusion are there with respect to its origin, distribution and species identification.

Although there is extensive literature on the wolf species, their ancient origin hypothesis is still not understood and is being debated. Indian wolf is genetically unique from all other wolves worldwide (5,6). It is hypothesized that the Himalayan wolf and the Indian gray wolf harbor most of the genetic diversity and are the most evolutionarily ancient lineages. They are being phylogenetically closer to jackal forms the basis for all other wolves and their divergence into different habitats (6).

Grey Wolf (Canis Lupus)

At present, only morphological and habitual behaviors are considered to trace their ancestral origin. However, studies based on the mitochondrial DNA sequences have indicated that the Indian gray wolf as the basal to all other extant Canis lupus haplotypes spaced out from the Himalayan wolf older-lineage (5,7). This basal position was further confirmed by comparing these sequences against worldwide wolf sequences (8,9,10). Likewise, a recent study was carried out to generate and compare the mitochondrial DNA sequences of ancient and modern wolves. The phylogenetic tree from the results indicated that both Indian gray wolf and the Himalayan wolf form the most basal (11). However, it is not possible to accept mtDNA alone as a basis for determining species status. Because, mitochondrial DNA sequences can only trace maternal lineages, and sometimes troubled with errors (12). In addition, most of the studies on Indian wolves involved wolves from India, which may not certainly refer to wolves with this old mtDNA sequence. Mitochondrial DNA is just a part of the genome, and what analyses of it actually prove are far narrower in scope than is often understood. While nuclear DNA studies are much harder to perform, but they are necessary before we start divining new species from those that have long been classified. Therefore, nuclear DNA investigations being done within Indian wolves is a must to interpret their ancestral lineage.

Genetic variation and its partitioning across populations provide information on the evolutionary history, demographic fluctuations, and population connectivity (13). More recently, genome-wide data are being analyzed to support an ancient or admixed origin hypothesis for the Holarctic gray wolf (Canis lupus) and the endemic coyote (Canis latrans) (14). They suggested the notion of unique ancestry as opposed to a hybrid origin. A rapidly advancing next-generation sequencing technologies has enabled the analysis of animal populations at the DNA sequence level (15). The next-generation sequencing is cost-effective and enables population-level studies of various organisms for the identification of their genotypic differences and phenotypic consequences (16). As a result, many large-scale population-based genome projects have been launched to analyze functional and evolutionary basis among animals such as tigers, dogs, forest elephants, chimpanzees, giant panda, etc. More recently, functional and evolutionary analysis of Korean bob-tailed native dog using whole-genome sequencing data has been successfully studied (16). However, attempts on analyzing the whole genome sequencing for Indian wolves is yet to be achieved. Till date, the genomic makeup or the present distribution of Indian wolves is not well characterized which is contributing problems to their ecological conservation.